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Daniel E. Weeks
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30
@daniel-e-weeks-10677
Last seen 11 months ago
Pittsburgh, Pennsylvania, United States…
When trying to run ChAMP version 1.8.2 on a data set of 91 samples using the default champ.process command, it got through the SVD step, but then died at the ComBat step:
Preparing files for ComBat Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed Calls: champ.process -> champ.runCombat In addition: Warning messages: 1: In min(beta2.v[selMR.idx]) : no non-missing arguments to min; returning Inf 2: In min(nbeta2.v[selMR.idx]) : no non-missing arguments to min; returning Inf 3: In min(beta2.v[selMR.idx]) : no non-missing arguments to min; returning Inf 4: In min(nbeta2.v[selMR.idx]) : no non-missing arguments to min; returning Inf 5: In min(beta2.v[selMR.idx]) : no non-missing arguments to min; returning Inf 6: In min(nbeta2.v[selMR.idx]) : no non-missing arguments to min; returning Inf Execution halted
In champ.norm, I see code like this:
if (min(beta.p, na.rm = TRUE) == 0) {
but in champ.runCombat, I see this (which lacks the na.rm option):
if (min(beta.c) == 0) {
I am not sure how to debug this.
Thank you.